Re: AMBER parameters

From: David A. Case <>
Date: Tue, 24 Jun 2003 08:25:35 -0700

On Tue, Jun 24, 2003, D Fernandez wrote:
> We are academic users of MacroModel Version 7.0.
> Two main problems appeared when the modeling study is
> started. Firstly, an error message informed us that the
> ffld has no parameters for the C-P bond. And second, it
> lacks parameters for the Mg cation. As the program fails
> to process the structure of interest, we ask you for the
> following:
> i) are there AMBER ffld parameters for the C-P bond? If
> so, how could they be obtained? Could be installed in
> MacroModel Version 7.0?

It may be best to address Macromodel-related questions to Schrodinger or
to some other list. Amber has a procedure (called "antechamber") to
derive force field parameters for arbitrary ligands. This is what
we advise our users to use. I don't know if there is any equivalent
thing in macromodel: perhaps you could use MMFF94, which has a similar

> ii) are there AMBER ffld parameters for magnesium?

Divalent ions are very difficult to handle in force fields, and there is
no agreed-upon set of parameters. You will probably have to do some
literature searching to find studies that somewhat match what you want to
do. Without knowing the details of your problem, it's hard to give advice.

...good luck....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Jun 24 2003 - 16:53:01 PDT
Custom Search